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processing all the wells in a column before going to next column #100

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processing all the wells in a column before going to next column #100

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8dac8ee
processing all the wells in a column before going to next column
FahimehMirhaj Aug 19, 2025
7ddfefd
Fixed the logic
FahimehMirhaj Aug 21, 2025
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18 changes: 11 additions & 7 deletions ...main/java/com/velox/sloan/cmo/workflows/kapalibrary/IndexBarcodeToSampleAutoAssigner.java
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Original file line number Diff line number Diff line change
Expand Up @@ -265,17 +265,21 @@ private void setLastIndexUsed(List<DataRecord> indexAssignmentConfigs, Integer o
* @param indexAssignmentConfigs
* @return int
*/
private int getStartIndexAssignmentConfigPosition(int lastUsedIndexPosition, List<DataRecord> indexAssignmentConfigs) throws ServerException, NotFound, RemoteException {
private int getStartIndexAssignmentConfigPosition(int lastUsedIndexPosition, List<DataRecord> indexAssignmentConfigs,
int plateSize) throws ServerException, NotFound, RemoteException {
if (lastUsedIndexPosition >= indexAssignmentConfigs.size() - 1) {
logInfo("Reached last Index, will start from first index position.");
return 0;
}
int nextIndexToUse = lastUsedIndexPosition + 1; //start with one index position after last index used.
for (int i = nextIndexToUse; i < indexAssignmentConfigs.size(); i++)
if (indexAssignmentConfigs.get(i).getStringVal("WellId", user).toUpperCase().contains("A")) {
return i;
}
return 0;
if ((plateSize == 96 && indexAssignmentConfigs.get(lastUsedIndexPosition).getStringVal("WellId", user).toUpperCase().contains("H"))
|| (plateSize == 384 && indexAssignmentConfigs.get(lastUsedIndexPosition).getStringVal("WellId", user).toUpperCase().contains("P"))) {
for (int i = nextIndexToUse; i < indexAssignmentConfigs.size(); i++)
if (indexAssignmentConfigs.get(i).getStringVal("WellId", user).toUpperCase().contains("A")) {
return i;
}
}
return nextIndexToUse;
}

/**
Expand Down Expand Up @@ -474,7 +478,7 @@ private void assignIndicesToSamples(List<DataRecord> indexAssignmentProtocolReco
boolean isCrisprOrAmpliconSeq = recipes.stream().anyMatch(RECIPES_TO_USE_SPECIAL_ADAPTERS::contains);
Integer positionOfLastUsedIndex = getPositionOfLastUsedIndex(indexAssignmentConfigs);
Double maxPlateVolume = autoHelper.getMaxVolumeLimit(plateSize);
Integer updatedLastIndexUsed = getStartIndexAssignmentConfigPosition(positionOfLastUsedIndex, indexAssignmentConfigs);
Integer updatedLastIndexUsed = getStartIndexAssignmentConfigPosition(positionOfLastUsedIndex, indexAssignmentConfigs, plateSize);
Set<String> indexAssignmentConfigPlatesToUse = new HashSet<>();
for (int i = updatedLastIndexUsed, j = 0; i < indexAssignmentConfigs.size() && j < indexAssignmentProtocolRecordsSortedColumnWise.size(); i++, j++) {
DataRecord indexAssignmentConfig = indexAssignmentConfigs.get(i);
Expand Down
1 change: 0 additions & 1 deletion ...in/java/com/velox/sloan/cmo/workflows/workflows/SmartSeq/CreateSequencingRequirments.java
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,6 @@ public PluginResult run() throws Exception {
Map<String, Object> values = new HashMap<>();
String sampleId = sample.getStringVal("SampleId", user);
String sampleName = sample.getStringVal("OtherSampleId", user);
String otherSampleId = sample.getStringVal("OtherSampleId", user);
String tumorOrNormal = sample.getStringVal("TumorOrNormal", user);
values.put("SampleId", sampleId);
values.put("SequencingRunType","PE100");
Expand Down